I think Apple should just force any such translation layer or
interpreter used in an application to be publicly available as
open-source. If one such meta-platform ever becomes a problem,
it’s easy for Apple to investigate the problem, and they can
even release a fixed version themselves. It doesn’t solve all
the problems people have with rule 3.3.1, but at least it’s not
an outright ban of technology, and it even promotes sharing your
building blocks with other developers (a good thing for the
platform if you ask me).

I suspect that an open source meta-platform is indeed more palatable to Apple than a proprietary one such as Flash, but I don’t think it fundamentally changes the problems Apple sees with such layers. Apple isn’t going to support such layers itself, open source or not. And while individual developers using such layers could, in theory — in a hypothetical future scenario where the intermediary layer becomes incompatible or incomplete — fix it themselves, that’s not realistic. Developers using something like, say, MonoTouch or Flash to write iPhone apps are not signing up to be responsible for future maintenance of the entire underlying framework they’re building upon. The whole reason they want to use these intermediary meta-platforms is because they think they’re making their jobs easier.